Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation

S Liu, CD Moon, N Zheng, S Huws, S Zhao, J Wang - Microbiome, 2022 - Springer
Although there is now an extensive understanding of the diversity of microbial life on earth
through culture-independent metagenomic DNA sequence analyses, the isolation and …

Fungal taxonomy and sequence-based nomenclature

R Lücking, MC Aime, B Robbertse, AN Miller… - Nature …, 2021 - nature.com
The identification and proper naming of microfungi, in particular plant, animal and human
pathogens, remains challenging. Molecular identification is becoming the default approach …

TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes

JP Meier-Kolthoff, JS Carbasse… - Nucleic acids …, 2022 - academic.oup.com
Microbial systematics is heavily influenced by genome-based methods and challenged by
an ever increasing number of taxon names and associated sequences in public data …

SeqCode: a nomenclatural code for prokaryotes described from sequence data

BP Hedlund, M Chuvochina, P Hugenholtz… - Nature …, 2022 - nature.com
Most prokaryotes are not available as pure cultures and therefore ineligible for naming
under the rules and recommendations of the International Code of Nomenclature of …

[HTML][HTML] Biosynthetic potential of the global ocean microbiome

L Paoli, HJ Ruscheweyh, CC Forneris, F Hubrich… - Nature, 2022 - nature.com
Natural microbial communities are phylogenetically and metabolically diverse. In addition to
underexplored organismal groups, this diversity encompasses a rich discovery potential for …

Multiple energy sources and metabolic strategies sustain microbial diversity in Antarctic desert soils

M Ortiz, PM Leung, G Shelley… - Proceedings of the …, 2021 - National Acad Sciences
Numerous diverse microorganisms reside in the cold desert soils of continental Antarctica,
though we lack a holistic understanding of the metabolic processes that sustain them. Here …

Scientific novelty beyond the experiment

JE Hallsworth, Z Udaondo, C Pedrós‐Alió… - Microbial …, 2023 - Wiley Online Library
Practical experiments drive important scientific discoveries in biology, but theory‐based
research studies also contribute novel—sometimes paradigm‐changing—findings. Here, we …

Genomes OnLine Database (GOLD) v. 8: overview and updates

S Mukherjee, D Stamatis, J Bertsch… - Nucleic acids …, 2021 - academic.oup.com
Abstract The Genomes OnLine Database (GOLD)(https://gold. jgi. doe. gov/) is a manually
curated, daily updated collection of genome projects and their metadata accumulated from …

Prokaryotic taxonomy and nomenclature in the age of big sequence data

P Hugenholtz, M Chuvochina, A Oren… - the ISME …, 2021 - academic.oup.com
The classification of life forms into a hierarchical system (taxonomy) and the application of
names to this hierarchy (nomenclature) is at a turning point in microbiology. The …

Verrucomicrobiota are specialist consumers of sulfated methyl pentoses during diatom blooms

LH Orellana, TB Francis, M Ferraro… - The ISME …, 2022 - academic.oup.com
Marine algae annually sequester petagrams of carbon dioxide into polysaccharides, which
are a central metabolic fuel for marine carbon cycling. Diatom microalgae produce sulfated …